"The terrorists have cells everywhere and they are active. We are continuing to pursue them," he told reporters, without giving details of specific targets.

DFAT warns the threat to Australians in Indonesia may reach beyond churches.

"Terrorists have previously attacked or planned to attack places where Westerners gather, including nightclubs, bars, restaurants, international hotels, airports and places of worship in Bali, Jakarta and elsewhere in Indonesia," it said.

"These types of venues could be targeted again."

There have been several attacks on Western targets in the past decade or so, including the 2002 Bali bombings which killed 202 people, including 88 Australians.

DFAT also notes that travellers to Indonesia could experience natural disasters like tsunamis, or be the victims of petty crime, drink-spiking and scams.

The advice does not recommend Australians stay away from Indonesia, but it does urge travellers to exercise a high degree of caution in the country.

However, Australians are urged to reconsider the need to travel to some areas including the provinces of Central Sulawesi, Maluku and Papua.